2017

Résumé: Seabirds are known to concentrate on prey patches or at predators aggregations standing for potential feeding opportunities. They may search for prey using olfaction or by detecting visually feeding con-specifics and sub-surface predators, or even boats. Thus, they might form a foraging network. We hypothesized that conditionally to the existence of a foraging network, the visual detection ability of seabirds should have a bearing on their medium-scale distribution at sea. Using a fishing-boat radar to catch the instantaneous distribution of seabirds groups within 30 km around the vessel, we conducted a spatial clustering of the seabird-echoes. We found 7,657 clusters (i.e. aggregations of echoes), lasting less than 15 minutes and measuring 9.2 km in maximum length (median). Distances between seabirds groups within clusters showed little variation (median: 2.1 km; CV: 0.5), while area varied largely (median: 21.9 km2; CV: 0.8). Given existing data on seabirds’ reaction distances to boats or other marine predators, we suggest that these structures may represent active foraging sequences of seabirds spreading themselves in space such as to possibly cue on each others. These seabird clusters were not previously described and are size compatible with the existence of a foraging network.

Résumé: Since the mid-1990s, drifting Fish Aggregating Devices (dFADs), artificial floating objects designed to aggregate fish, have become an important mean by which purse seine fleets catch tropical tunas. Mass deployment of dFADs, as well as the massive use of GPS buoys to track dFADs and natural floating objects, has raised serious concerns for the state of tropical tuna stocks and ecosystem functioning. Here, we combine tracks from a large proportion of the French GPS buoys from the Indian and Atlantic oceans with data from observers aboard French and Spanish purse seiners and French logbook data to estimate the total number of dFADs and GPS buoys used within the main fishing grounds of these two oceans over the period 2007-2013. In the Atlantic Ocean, the total number of dFADs increased from 1175 dFADs active in January 2007 to 8575 dFADs in August 2013. In the Indian Ocean, this number increased from 2250 dFADs in October 2007 to 10 300 dFADs in September 2013. In both oceans, at least a fourfold increase in the number of dFADs was observed over the 7-year study period. Though the relative proportion of natural to artificial floating objects varied over space, with some areas such as the Mozambique Channel and areas adjacent to the mouths of the Niger and Congo rivers being characterized by a relatively high percentage of natural objects, in no region do dFADs represent <50% of the floating objects and the proportion of natural objects has dropped over time as dFAD deployments have increased. Globally, this increased dFAD use represents a major change to the pelagic ecosystem that needs to be closely followed in order to assess its impacts and avoid negative ecosystem consequences.

2016

Résumé: In this introductory paper we highlight key questions that were discussed during the symposium on “Status, functioning and shifts in marine ecosystems” organized by the Association Francaise d'Halieutique (French Association for Fisheries Sciences, Montpellier, France, July 2015). This symposium illustrated that fisheries science is now working at multiple scales and on all dimensions of socio-ecosystems (ecological, political, sociological, and economic), with a great diversity of approaches and taking into account different levels of complexity while acknowledging diverse sources of uncertainty. We argue that we should go one step further and call for a protean fisheries science to address the deteriorated states of aquatic ecosystems caused by anthropogenic pressures. Protean science is constantly evolving to meet emerging issues, while improving its coherence and integration capacity in its complexity. This science must be nourished by multiple approaches and be capable of addressing all organizational scales, from individual fish or fishermen up to the entire ecosystem, include society, its economy and the services it derives from aquatic systems. Such a protean science is required to address the complexity of ecosystem functioning and of the impacts of anthropogenic pressures.

Résumé: ABSTRACT: An improved knowledge of habitat utilization by demersal species is a pre-requisite for their spatial management. Based on scientific survey data collected over the period 1994-2010, the present study investigates relationships between 4 environmental factors and 10 demersal species in the Gulf of Lions (northwestern Mediterranean Sea). Generalized linear models provided statistically satisfying results in terms of both model explanatory and predictive powers. The ‘biological zone’ factors, based on the percentage of light penetration to the sea bottom and bottom temperature, were the most important factors, while sediments and benthic macrofauna were only significant for a few species. The type of associations varied among species, resulting in different spatial predictions among species. The spatial structures of species distributions appeared to be due more to habitat preferences that are spatially auto-correlated than to intra-specific population dynamics. The use of a spatial optimization procedure on the predicted species distributions allowed the detection of a set of 7 zones covering 17% of the studied region, that included at least 20% of each species’ abundance and that reflected the diversity of the species’ habitats. This preliminary result illustrates the potential of further analyses on Marine Protected Areas as a tool for the conservation of the demersal community in this region.

2015

Résumé: * Mapping diversity indices, that is estimating values in all locations of a given area from some sampled locations, is central to numerous research and applied fields in ecology. * Two approaches are used to map diversity indices without including abiotic or biotic variables: (i) the indirect approach, which consists in estimating each individual species distribution over the area, then stacking the distributions of all species to estimate and map a posteriori the diversity index, (ii) the direct approach, which relies on computing a diversity index in each sampled locations and then to interpolate these values to all locations of the studied area for mapping. * For both approaches, we document drawbacks from theoretical and practical viewpoints and argue about the need for adequate interpolation methods. First, we point out that the indirect approach is problematic because of the high proportion of rare species in natural communities. This leads to zero-inflated distributions, which cannot be interpolated using standard statistical approaches. Secondly, the direct approach is inaccurate because diversity indices are not spatially additive, that is the diversity of a studied area (e.g. region) is not the sum of the local diversities. Therefore, the arithmetic variance and some of its derivatives, such as the variogram, are not appropriate to ecologically measure variation in diversity indices. For the direct approach, we propose to consider the β-diversity, which quantifies diversity variations between locations, by the mean of a β-gram within the interpolation procedure. We applied this method, as well as the traditional interpolation methods for comparison purposes on different faunistic and floristic data sets collected from scientific surveys. We considered two common diversity indices, the species richness and the Rao's quadratic entropy, knowing that the above issues are true for complementary species diversity indices as well as those dealing with other biodiversity levels such as genetic diversity. * We conclude that none of the approaches provided an accurate mapping of diversity indices and that further methodological developments are still needed. We finally discuss lines of research that may resolve this key issue, dealing with conditional simulations and models taking into account biotic and abiotic explanatory variables.

Résumé: Increasing human pressures and global environmental change may severely affect the diversity of species assemblages and associated ecosystem services. Despite the recent interest in phylogenetic and functional diversity, our knowledge on large spatio-temporal patterns of demersal fish diversity sampled by trawling remains still incomplete, notably in the Mediterranean Sea, one of the most threatened marine regions of the world. We investigated large spatio-temporal diversity patterns by analysing a dataset of 19,886 hauls from 10 to 800 m depth performed annually during the last two decades by standardized scientific bottom trawl field surveys across the Mediterranean Sea, within the MEDITS program. A multi-component (eight diversity indices) and multi-scale (local assemblages, biogeographic regions to basins) approach indicates that only the two most traditional components (species richness and evenness) were sufficient to reflect patterns in taxonomic, phylogenetic or functional richness and divergence. We also put into question the use of widely computed indices that allow comparing directly taxonomic, phylogenetic and functional diversity within a unique mathematical framework. In addition, demersal fish assemblages sampled by trawl do not follow a continuous decreasing longitudinal/latitudinal diversity gradients (spatial effects explained up to 70.6% of deviance in regression tree and generalized linear models), for any of the indices and spatial scales analysed. Indeed, at both local and regional scales species richness was relatively high in the Iberian region, Malta, the Eastern Ionian and Aegean seas, meanwhile the Adriatic Sea and Cyprus showed a relatively low level. In contrast, evenness as well as taxonomic, phylogenetic and functional divergences did not show regional hotspots. All studied diversity components remained stable over the last two decades. Overall, our results highlight the need to use complementary diversity indices through different spatial scales when developing conservation strategies and defining delimitations for protected areas.

Résumé: In the open ocean, movements of migratory fish populations are typically surveyed using tagging methods that are subject to low sample sizes for archive tags, except for a few notable examples, and poor temporal resolution for conventional tags. Alternatively, one can infer patterns of movement of migratory fish by tracking movements of their predators, i.e., fishing vessels, whose navigational systems (e.g., GPS) provide accurate and frequent VMS (vessel monitoring system) records of movement in pursuit of prey. In this paper, we develop a state-space model that infers the foraging activities of fishing vessels from their tracks. Second, we link foraging activities to probabilities of tuna presence. Finally, using multivariate geostatistical interpolation (cokriging) we map the probability of tuna presence together with their estimation variances and produce a time series of indices of abundance. While the segmentation of the trajectories is validated by observers' data, the present VMS-index is compared to catch rate and proved to be useful for management perspectives. The approach reported in this manuscript extends beyond the case study considered. It can be applied to any foragers that engage in an attempt of capture when they see prey and for whom this attempt is linked to a tractable change in behavior.

2014

Bez, N., and C. B. Braham. "Indicator variables for a robust estimation of an acoustic index of abundance." Canadian Journal of Fisheries and Aquatic Sciences. 71.5 (2014): 709–718.

Résumé: In North West Africa, pelagic fisheries are an essential economic sector. However, the scientific community fails to perform satisfactory assessments of key pelagic species like sardinella, owing to a lack of relevant indices of abundance to tune the model. This paper provides an alternative acoustic index based on a semiquantitative modelisation of acoustic densities. Acoustic energy is split into binomial variables coding for null, low, medium, large, and very large densities. A multivariate geostatistical approach allows (i) mapping the spatial distribution of classes of densities and (ii) computing a new acoustic index of abundance for Sardinella aurita and Sardinella maderensis. We used the surveys of RV Fridtjof Nansen (1995-2006) and RV Al-Awam (2007-2010). Our results indicated that empirical spatial structures were highly stable over time for both between areas and surveys. Co-kriging maps also showed that sardinella had stable hot spots of distribution. The indices of abundance developed in the present study were tested in an assessment procedure and outperformed all the indices used routinely by the FAO-CECAF (Fishery Committee for the Eastern Central Atlantic) assessment working group.

Résumé: Sardinella spp. are the main species fished in Mauritanian waters. Logbook data (1991&8211;2009) were used to standardise CPUE. This clearly revealed that the abundance of sardinella peaked in the warm season (July&8211;September) which is the main, if not the only significant spawning season for round sardinella.
This study does not directly confirm or falsify the common belief that the adults migrate from the Senegalese EEZ up to north of the 21° N latitude, but it presents a variety of new hypotheses. If a single transboundary stock exists, part of its individuals, or a sub-stock, is probably more sedentary and remains in the permanent upwelling area located in northern Mauritania and southern Morocco.
Between years, changes in abundance index are dominated by a decrease from 1996 to 2006, depending on the months taken into account, and especially whether or not the warm (spawning) season is considered. For a given month, the spatial distribution of sardinella shows limited differences between years. In the southernmost latitudes of the Mauritanian EEZ the seasonal pattern, which is dominated by high catch rates during the warm season, is much stronger after the year 2001, and then tended to increase year after year.
Changes in species distribution and abundance during the twenty-year study period are difficult to relate to environmental dynamics. However, an inversion of the upwelling trend was observed in 2001, matching a change in the seasonality of sardinella catches, although the causality between the two phenomena could not be established. The increase in the abundance index of sardinella in the last five years, particularly during most of the core fishing season (July&8211;September) might be due to favourable oceanographic conditions (higher upwelling index) and/or changes in the fishing strategies or efficiency. Before annual indices of abundance can be used in the future, it will be necessary to better understand possible changes in catchability during the warm/spawning season.

Résumé: The desire to predict the consequences of global environmental change has been the driver towards more realistic models embracing the variability and uncertainties inherent in ecology. Statistical ecology has gelled over the past decade as a discipline that moves away from describing patterns towards modelling the ecological processes that generate these patterns. Following the fourth International Statistical Ecology Conference (1–4 July 2014) in Montpellier, France, we analyse current trends in statistical ecology. Important advances in the analysis of individual movement, and in the modelling of population dynamics and species distributions, are made possible by the increasing use of hierarchical and hidden process models. Exciting research perspectives include the development of methods to interpret citizen science data and of efficient, flexible computational algorithms for model fitting. Statistical ecology has come of age: it now provides a general and mathematically rigorous framework linking ecological theory and empirical data.

Résumé: Understanding the ecological and anthropogenic drivers of population dynamics requires detailed studies on habitat selection and spatial distribution. Although small pelagic fish aggregate in large shoals and usually exhibit important spatial structure, their dynamics in time and space remain unpredictable and challenging. In the Gulf of Lions (north-western Mediterranean), sardine and anchovy biomasses have declined over the past 5 years causing an important fishery crisis while sprat abundance rose. Applying geostatistical tools on scientific acoustic surveys conducted in the Gulf of Lions, we investigated anchovy, sardine and sprat spatial distributions and structures over 10 years. Our results show that sardines and sprats were more coastal than anchovies. The spatial structure of the three species was fairly stable over time according to variogram outputs, while year-to-year variations in kriged maps highlighted substantial changes in their location. Support for the McCall's basin hypothesis (covariation of both population density and presence area with biomass) was found only in sprats, the most variable of the three species. An innovative method to investigate species collocation at different scales revealed that globally the three species strongly overlap. Although species often co-occurred in terms of presence/absence, their biomass density differed at local scale, suggesting potential interspecific avoidance or different sensitivity to local environmental characteristics. Persistent favourable areas were finally detected, but their environmental characteristics remain to be determined.

Résumé: This study analyzes the temporal variability/stability of the spatial distributions of key exploited species in the Gulf of Lions (Northwestern Mediterranean Sea). To do so, we analyzed data from the MEDITS bottom-trawl scientific surveys from 1994 to 2010 at 66 fixed stations and selected 12 key exploited species. We proposed a geostatistical approach to handle zero-inflated and non-stationary distributions and to test for the temporal stability of the spatial structures. Empirical Orthogonal Functions and other descriptors were then applied to investigate the temporal persistence and the characteristics of the spatial patterns. The spatial structure of the distribution (i.e. the pattern of spatial autocorrelation) of the 12 key species studied remained highly stable over the time period sampled. The spatial distributions of all species obtained through kriging also appeared to be stable over time, while each species displayed a specific spatial distribution. Furthermore, adults were generally more densely concentrated than juveniles and occupied areas included in the distribution of juveniles. Despite the strong persistence of spatial distributions, we also observed that the area occupied by each species was correlated to its abundance: the more abundant the species, the larger the occupation area. Such a result tends to support MacCall's basin theory, according to which density-dependence responses would drive the expansion of those 12 key species in the Gulf of Lions. Further analyses showed that these species never saturated their habitats, suggesting that they are below their carrying capacity; an assumption in agreement with the overexploitation of several of these species. Finally, the stability of their spatial distributions over time and their potential ability to diffuse outside their main habitats give support to Marine Protected Areas as a potential pertinent management tool.

Résumé: Background is provided to the selection of ecological indicators by the IndiSeas Working Group, and the methodology adopted for analysis and comparison of indicators across exploited marine ecosystems is documented. The selected indicators are presented, how they are calculated is explained, and the philosophy behind the comparative approach is given. The combination of selected indicators is intended to reflect different dynamics, tracking processes that display differential responses to fishing, and is meant to provide a complementary means of assessing marine ecosystem trends and states. IndiSeas relied on inputs and insights provided by the local experts from participating ecosystems, helping to understand state and trend indicators and to disentangle the effect of other potential ecosystem drivers, such as climate variability. This project showed that the use of simple and available indicators under an ecosystem approach can achieve a real, wide-reaching evaluation of marine ecosystem status caused by fishing. This is important because the socio-economics of areas where fishing activities develop differs significantly around the globe, and in many countries, insufficient data are available for complex and exhaustive analyses.

Résumé: Converging results in different scientific fields (behavioural ecology, fisheries biology, acoustic tagging, fisheries acoustics, behavioural modelling) suggest the existence of “micro-groups” inside fish schools. These would comprise a few (5-10) fish maintaining contact during a period long enough to allow individuals to recognise each other. It is hypothesised that they would prefer to share the space with familiar rather than anonymous conspecifics. To evaluate whether acoustic methods could be used to recognise “micro-structures” inside fish schools and help test the “micro-group” hypothesis we analysed acoustic data from anchovy schools off Peru, and gadoids in the North Sea. Data collection used a multibeam sonar (Reson SeaBat 6012). In the Peruvian case study, the sonar was mounted set horizontally on a drifting research vessel and the internal structure of the schools of anchovies was analysed, although individual fish could not be discriminated. In the North Sea case study, the sonar was orientated vertically above a demersal trawl to allow observation of individual fish entering the trawl. Geostatistical analyses were used to evaluate the existence of small spatial structures in anchovy schools. In these schools, “micro-structures” with a scale as small as 0.5 m were observed acoustically. For the gadoids nearest neighbour distance (NDD) measurements were carried out, suggesting that the fish aggregated in small groups (2 to 25 individuals, with an average of 3.7 fish per group) in the trawl catches. The perspectives and limitations of these results are discussed.

Résumé: Background is provided to the selection of ecological indicators by the IndiSeas Working Group, and the methodology adopted for analysis and comparison of indicators across exploited marine ecosystems is documented. The selected indicators are presented, how they are calculated is explained, and the philosophy behind the comparative approach is given. The combination of selected indicators is intended to reflect different dynamics, tracking processes that display differential responses to fishing, and is meant to provide a complementary means of assessing marine ecosystem trends and states. IndiSeas relied on inputs and insights provided by the local experts from participating ecosystems, helping to understand state and trend indicators and to disentangle the effect of other potential ecosystem drivers, such as climate variability. This project showed that the use of simple and available indicators under an ecosystem approach can achieve a real, wide-reaching evaluation of marine ecosystem status caused by fishing. This is important because the socio-economics of areas where fishing activities develop differs significantly around the globe, and in many countries, insufficient data are available for complex and exhaustive analyses.

Résumé: In the context of the expansion of animal tracking and bio-logging, state-space models have been developed with the objective to characterise animals' trajectories and to understand the factors controlling their behaviour. In the fisheries community, the electronic tagging of vessels commonly designated by Vessel Monitoring Systems (VMS) is developing and provides a new insight for the understanding, the analysis and the modelling of the trajectories of vessels and their prospecting behaviour. VMS data are thus a clue for the proper definition of fishing effort which remains a fundamental parameter of tuna stock assessments. In this context, we used the VMS (recording of hourly positions) of the French tropical tuna purse-seiners operating in the Indian Ocean to characterise three types of movement (states) on the VMS trajectories (stillness, tracking, and cruising). Based on empirical evidences, and on the regular frequency of VMS acquisition, this was achieved by the development of a Bayesian Hidden Markov model for the speeds and turning angles derived from the hourly steps of the trajectories. In a second phase, states were related to activities disentangling stillness into fishing or stop at sea. Finally the quality of the model performances was rigorously quantified thanks to observers' data. Confronting model prediction and true activities allowed estimating that 10% of the hourly steps were misclassified. The assumptions and model' choices are discussed, highlighting the fact that VMS data and observers' data having different time resolutions, the effective use of validating data was troublesome. However, without validation, these analyses remain speculative. The validation part of this work represents an important step for the operational use of state-space models in ecology in the broad sense (predators' tracking data, e.g. birds or mammals trajectories).